GEO DataSets

(Submitter supplied) Gene expression plasticity allows bacteria to adapt to diverse environments, tie their metabolism to available nutrients, and cope with stress. This is particularly relevant in a niche as dynamic and hostile as the human intestinal tract, yet transcriptional networks remain largely unknown in gut Bacteroides spp. Here, we map transcriptional units and profile their expression levels in Bacteroides thetaiotaomicron over a suite of 15 defined experimental conditions that are relevant in vivo, such as variation of temperature, pH, and oxygen tension, exposure to antibiotic stress, and growth on simple carbohydrates or on host mucin-derived glycans. more...

Organism:

Bacteroides thetaiotaomicron

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28094

40 Samples

Download data: CSV, XLSX

(Submitter supplied) The aim of this RNA-sequencing study is to measure differential gene expression in 4 intestinal bacteria (Bacteroides xylanisolvens, Bacteroides thetaiotaomicron, Subdoligranulum variabile and Roseburia intestinalis). The data highlight the coordinated action of genes within the same locus involved in the degradation of complex carbohydrates. These loci are well characterized in Bacteroidetes species and referred to as polysaccharide utilization loci. more...

Organism:

Bacteroides thetaiotaomicron; Roseburia intestinalis; Subdoligranulum variabile; Bacteroides xylanisolvens

Type:

Expression profiling by high throughput sequencing

4 related Platforms

36 Samples

Download data: CSV

(Submitter supplied) Microbiota-centric interventions are limited by our incomplete understanding of the gene functions of many of its constituent species. This applies in particular to small RNAs (sRNAs), which are emerging as important regulators in microbiota species yet tend to be missed by traditional functional genomics approaches. Here, we establish CRISPR interference (CRISPRi) in the abundant microbiota member Bac-teroides thetaiotaomicron for genome-wide sRNA screens. more...

Organism:

Bacteroides thetaiotaomicron

Type:

Other

Platforms:

GPL33520 GPL28094

9 Samples

Download data: FASTA, TXT

(Submitter supplied) Gram-negative, obligate anaerobic Bacteroides thetaiotaomicron is emerging as the model organism for gut microbiota research. Colonization of its host niche within the human colon depends to large parts on the extensive metabolic capacity encoded in the Bacteroides genome, but little is known about how its transcription is organized. Here, we transferred differential RNA-seq (dRNA-seq) to B. thetaiotaomicron type strain VPI-5482 to globally map transcription start sites (TSSs). more...

Organism:

Bacteroides thetaiotaomicron

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28094

24 Samples

Download data: WIG, XLSX